1
|
Chua GNL, Liu S. When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions. Annu Rev Biophys 2024; 53:169-191. [PMID: 38237015 DOI: 10.1146/annurev-biophys-030822-032904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities-often central to the protein function-thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein-DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field.
Collapse
Affiliation(s)
- Gabriella N L Chua
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
- Tri-Institutional PhD Program in Chemical Biology, New York, New York, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, New York, USA;
| |
Collapse
|
2
|
Molina M, Way LE, Ren Z, Liao Q, Guerra B, Shields B, Wang X, Kim H. A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments. CELL REPORTS METHODS 2023; 3:100614. [PMID: 37832544 PMCID: PMC10626211 DOI: 10.1016/j.crmeth.2023.100614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/28/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed an in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK tag substantially altered ParB's DNA compaction rates and its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. While it is typically assumed that short peptide tags minimally perturb protein function, our results urge researchers to carefully validate the use of tags for protein labeling. Our comprehensive analysis can be expanded and used as a guide to assess the impacts of other tags on DNA-binding proteins in single-molecule assays.
Collapse
Affiliation(s)
- Miranda Molina
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA; Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Lindsey E Way
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Zhongqing Ren
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Qin Liao
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA
| | - Bianca Guerra
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Brandon Shields
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Xindan Wang
- Department of Biology, Indiana University, 1001 E 3(rd) St., Bloomington, IN 47405, USA.
| | - HyeongJun Kim
- Biochemistry and Molecular Biology Program, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA; Department of Physics and Astronomy, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA.
| |
Collapse
|
3
|
Liang J, Li J, Zhong Z, Rujiralai T, Ma J. Quantifying the force in flow-cell based single-molecule stretching experiments. NANOSCALE 2021; 13:15916-15927. [PMID: 34522927 DOI: 10.1039/d1nr04748e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The flow-cell based single-molecule manipulation technique has found many applications in the study of DNA mechanics and protein-DNA interactions. However, the force in these experiments has not been fully characterized and is usually limited to a moderate force regime (<25 pN). In this work, using the "tethered-bead" assay, the hydrodynamic drag of DNA has been quantitatively evaluated based on a "bead-spring chain" model. The force derived from the Brownian motion of the bead thus contains both contributions from this equivalent hydrodynamic drag of DNA and the pulling force from the tethered bead. Next, using flow-cell based DNA pulling experiments, the linear relationship between the flow rate and total hydrodynamic force on the bead-DNA system has been demonstrated to be valid over a wide force range (0-110 pN). Consequently, the force can be directly converted from the flow rate by a linear factor that can be calibrated either by the bead's Brownian motion at low flow rates or using DNA overstretching transition. Furthermore, the hydrodynamic force and torque due to the shear flow on the bead as well as the equivalent stretching force on DNA are calculated based on theoretical models with the hydrodynamic drag on DNA also considered. The calculated force-extension curves show a good agreement with the measured ones. These results offer important insights into the force in flow-cell based single-molecule stretching experiments and provide a foundation for establishing flow-cells as a simple, low-cost, yet flexible and precise tool for single-molecule force measurements over a wide force range.
Collapse
Affiliation(s)
- Jialun Liang
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Jiaxi Li
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Zhensheng Zhong
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Thitima Rujiralai
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| |
Collapse
|
4
|
Babamohammadi S, Lillian TD. Traveling Salesman Finds Random Walk: A Curve Reconstruction Algorithm for Supercoiled DNA. Biophys J 2020; 119:2517-2523. [PMID: 33217387 DOI: 10.1016/j.bpj.2020.10.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 09/26/2020] [Accepted: 10/19/2020] [Indexed: 11/25/2022] Open
Abstract
DNA supercoiling plays an important role in a variety of cellular processes, including transcription, replication, and DNA compaction. To fully understand these processes, we must uncover and characterize the dynamics of supercoiled DNA. However, supercoil dynamics are difficult to access because of the wide range of relevant length and timescales. In this work, we present an algorithm to reconstruct the arrangement of identical fluorescent particles distributed around a circular DNA molecule, given their three-dimensional trajectories through time. We find that this curve reconstruction problem is analogous to solving the traveling salesman problem. We demonstrate that our approach converges to the correct arrangement with a sufficiently long observation time. In addition, we show that the time required to accurately reconstruct the fluorophore arrangement is reduced by increasing the fluorophore density or reducing the level of supercoiling. This curve reconstruction algorithm, when paired with next-generation super-resolution imaging systems, could be used to access and thereby advance our understanding of supercoil dynamics.
Collapse
Affiliation(s)
- Saeed Babamohammadi
- Department of Mechanical Engineering, Shahrood University of Technology, Shahrood, Semnan, Iran
| | - Todd D Lillian
- William B. Burnsed, Jr. Department of Mechanical, Aerospace, and Biomedical Engineering, University of South Alabama, Mobile, Alabama.
| |
Collapse
|
5
|
Piatt SC, Loparo JJ, Price AC. The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI. Biophys J 2019; 116:2367-2377. [PMID: 31113551 PMCID: PMC6588823 DOI: 10.1016/j.bpj.2019.04.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 02/02/2023] Open
Abstract
A one-dimensional (1D) search is an essential step in DNA target recognition. Theoretical studies have suggested that the sequence dependence of 1D diffusion can help resolve the competing demands of a fast search and high target affinity, a conflict known as the speed-selectivity paradox. The resolution requires that the diffusion energy landscape is correlated with the underlying specific binding energies. In this work, we report observations of a 1D search by quantum dot-labeled EcoRI. Our data supports the view that proteins search DNA via rotation-coupled sliding over a corrugated energy landscape. We observed that whereas EcoRI primarily slides along DNA at low salt concentrations, at higher concentrations, its diffusion is a combination of sliding and hopping. We also observed long-lived pauses at genomic star sites, which differ by a single nucleotide from the target sequence. To reconcile these observations with prior biochemical and structural data, we propose a model of search in which the protein slides over a sequence-independent energy landscape during fast search but rapidly interconverts with a "hemispecific" binding mode in which a half site is probed. This half site interaction stabilizes the transition to a fully specific mode of binding, which can then lead to target recognition.
Collapse
Affiliation(s)
- Sadie C Piatt
- Department of Chemistry and Physics, Emmanuel College, Boston, Massachusetts
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts.
| | - Allen C Price
- Department of Chemistry and Physics, Emmanuel College, Boston, Massachusetts.
| |
Collapse
|
6
|
King G, Biebricher AS, Heller I, Peterman EJG, Wuite GJL. Quantifying Local Molecular Tension Using Intercalated DNA Fluorescence. NANO LETTERS 2018; 18:2274-2281. [PMID: 29473755 PMCID: PMC6023266 DOI: 10.1021/acs.nanolett.7b04842] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/14/2018] [Indexed: 05/25/2023]
Abstract
The ability to measure mechanics and forces in biological nanostructures, such as DNA, proteins and cells, is of great importance as a means to analyze biomolecular systems. However, current force detection methods often require specialized instrumentation. Here, we present a novel and versatile method to quantify tension in molecular systems locally and in real time, using intercalated DNA fluorescence. This approach can report forces over a range of at least ∼0.5-65 pN with a resolution of 1-3 pN, using commercially available intercalating dyes and a general-purpose fluorescence microscope. We demonstrate that the method can be easily implemented to report double-stranded (ds)DNA tension in any single-molecule assay that is compatible with fluorescence microscopy. This is particularly useful for multiplexed techniques, where measuring applied force in parallel is technically challenging. Moreover, tension measurements based on local dye binding offer the unique opportunity to determine how an applied force is distributed locally within biomolecular structures. Exploiting this, we apply our method to quantify the position-dependent force profile along the length of flow-stretched DNA and reveal that stretched and entwined DNA molecules-mimicking catenated DNA structures in vivo-display transient DNA-DNA interactions. The method reported here has obvious and broad applications for the study of DNA and DNA-protein interactions. Additionally, we propose that it could be employed to measure forces in any system to which dsDNA can be tethered, for applications including protein unfolding, chromosome mechanics, cell motility, and DNA nanomachines.
Collapse
|
7
|
Nir G, Chetrit E, Vivante A, Garini Y, Berkovich R. The role of near-wall drag effects in the dynamics of tethered DNA under shear flow. SOFT MATTER 2018; 14:2219-2226. [PMID: 29451293 DOI: 10.1039/c7sm01328k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We utilized single-molecule tethered particle motion (TPM) tracking, optimized for studying the behavior of short (0.922 μm) dsDNA molecules under shear flow conditions, in the proximity of a wall (surface). These experiments track the individual trajectories through a gold nanobead (40 nm in radius), attached to the loose end of the DNA molecules. Under such circumstances, local interactions with the wall become more pronounced, manifested through hydrodynamic interactions. To elucidate the mechanical mechanism that affects the statistics of the molecular trajectories of the tethered molecules, we estimate the resting diffusion coefficient of our system. Using this value and our measured data, we calculate the orthogonal distance of the extended DNA molecules from the surface. This calculation considers the hydrodynamic drag effect that emerges from the proximity of the molecule to the surface, using the Faxén correction factors. Our finding enables the construction of a scenario according to which the tension along the chain builds up with the applied shear force, driving the loose end of the DNA molecule away from the wall. With the extension from the wall, the characteristic times of the system decrease by three orders of magnitude, while the drag coefficients decay to a plateau value that indicates that the molecule still experiences hydrodynamic effects due to its proximity to the wall.
Collapse
Affiliation(s)
- Guy Nir
- Dep. of Genetics, Harvard Medical School, Boston, MA 02115, USA. and Department of Physics and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel
| | - Einat Chetrit
- Department of Chemical-Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
| | - Anat Vivante
- Department of Physics and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel
| | - Yuval Garini
- Department of Physics and Institute of Nanotechnology, Bar Ilan University, Ramat Gan 52900, Israel
| | - Ronen Berkovich
- Department of Chemical-Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel. and The Ilze Katz Institute for Nanoscience and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| |
Collapse
|
8
|
Madariaga-Marcos J, Hormeño S, Pastrana CL, Fisher GLM, Dillingham MS, Moreno-Herrero F. Force determination in lateral magnetic tweezers combined with TIRF microscopy. NANOSCALE 2018; 10:4579-4590. [PMID: 29461549 PMCID: PMC5831119 DOI: 10.1039/c7nr07344e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/07/2017] [Indexed: 06/08/2023]
Abstract
Combining single-molecule techniques with fluorescence microscopy has attracted much interest because it allows the correlation of mechanical measurements with directly visualized DNA : protein interactions. In particular, its combination with total internal reflection fluorescence microscopy (TIRF) is advantageous because of the high signal-to-noise ratio this technique achieves. This, however, requires stretching long DNA molecules across the surface of a flow cell to maximize polymer exposure to the excitation light. In this work, we develop a module to laterally stretch DNA molecules at a constant force, which can be easily implemented in regular or combined magnetic tweezers (MT)-TIRF setups. The pulling module is further characterized in standard flow cells of different thicknesses and glass capillaries, using two types of micrometer size superparamagnetic beads, long DNA molecules, and a home-built device to rotate capillaries with mrad precision. The force range achieved by the magnetic pulling module was between 0.1 and 30 pN. A formalism for estimating forces in flow-stretched tethered beads is also proposed, and the results compared with those of lateral MT, demonstrating that lateral MT achieve higher forces with lower dispersion. Finally, we show the compatibility with TIRF microscopy and the parallelization of measurements by characterizing DNA binding by the centromere-binding protein ParB from Bacillus subtilis. Simultaneous MT pulling and fluorescence imaging demonstrate the non-specific binding of BsParB on DNA under conditions restrictive to condensation.
Collapse
Affiliation(s)
- J. Madariaga-Marcos
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
| | - S. Hormeño
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
| | - C. L. Pastrana
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
| | - G. L. M. Fisher
- DNA:Protein Interactions Unit , School of Biochemistry , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK
| | - M. S. Dillingham
- DNA:Protein Interactions Unit , School of Biochemistry , Biomedical Sciences Building , University of Bristol , Bristol , BS8 1TD , UK
| | - F. Moreno-Herrero
- Department of Macromolecular Structures , Centro Nacional de Biotecnología , Consejo Superior de Investigaciones Científicas , 28049 Cantoblanco , Madrid , Spain .
| |
Collapse
|
9
|
Kim H, Loparo JJ. Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-Stretching with Single-Molecule Imaging. Methods Mol Biol 2018; 1837:277-299. [PMID: 30109616 DOI: 10.1007/978-1-4939-8675-0_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nucleoid-associated proteins bind to DNA specifically and nonspecifically to perform various roles in chromosome organization and segregation. In this chapter, we describe how the interaction between nucleoid-associated proteins and flow-stretched DNAs can be visualized on the single-molecule level. We describe three different experimental schemes that allow one to directly observe how these proteins that make up bacterial chromatin, associate with and act on DNAs. First, we describe how to visualize the diffusion of fluorescently labeled proteins on flow stretched DNAs. Second, we describe how the binding of bacterial chromatin proteins can be correlated with DNA condensation. Lastly, we describe the DNA motion capture assay, which allows one to probe the mechanism of DNA condensation by tracking how different segments of a flow stretched DNA are compacted by bacterial chromatin proteins.
Collapse
Affiliation(s)
- HyeongJun Kim
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
10
|
Kim Y, de la Torre A, Leal AA, Finkelstein IJ. Efficient modification of λ-DNA substrates for single-molecule studies. Sci Rep 2017; 7:2071. [PMID: 28522818 PMCID: PMC5437064 DOI: 10.1038/s41598-017-01984-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/05/2017] [Indexed: 01/15/2023] Open
Abstract
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA. A set of PCR cassettes facilitates the introduction of recombinant DNA sequences into the λ-phage genome with 90-100% yield. Extrahelical structures and chemical modifications can be inserted at user-defined sites via an improved nicking enzyme-based strategy. As a proof-of-principle, we explore the interactions of S. cerevisiae Proliferating Cell Nuclear Antigen (yPCNA) with modified DNA sequences and structures incorporated within λ-DNA. Our results demonstrate that S. cerevisiae Replication Factor C (yRFC) can load yPCNA onto 5'-ssDNA flaps, (CAG)13 triplet repeats, and homoduplex DNA. However, yPCNA remains trapped on the (CAG)13 structure, confirming a proposed mechanism for triplet repeat expansion. We anticipate that this molecular toolbox will be broadly useful for other studies that require site-specific modification of long DNA substrates.
Collapse
Affiliation(s)
- Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Armando de la Torre
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Andrew A Leal
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
| |
Collapse
|
11
|
Song D, Graham TGW, Loparo JJ. A general approach to visualize protein binding and DNA conformation without protein labelling. Nat Commun 2016; 7:10976. [PMID: 26952553 PMCID: PMC4786781 DOI: 10.1038/ncomms10976] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/08/2016] [Indexed: 01/29/2023] Open
Abstract
Single-molecule manipulation methods, such as magnetic tweezers and flow stretching, generally use the measurement of changes in DNA extension as a proxy for examining interactions between a DNA-binding protein and its substrate. These approaches are unable to directly measure protein–DNA association without fluorescently labelling the protein, which can be challenging. Here we address this limitation by developing a new approach that visualizes unlabelled protein binding on DNA with changes in DNA conformation in a relatively high-throughput manner. Protein binding to DNA molecules sparsely labelled with Cy3 results in an increase in fluorescence intensity due to protein-induced fluorescence enhancement (PIFE), whereas DNA length is monitored under flow of buffer through a microfluidic flow cell. Given that our assay uses unlabelled protein, it is not limited to the low protein concentrations normally required for single-molecule fluorescence imaging and should be broadly applicable to studying protein–DNA interactions. Single-molecule imaging of protein-DNA association requires fluorescently labelled protein, which limits the protein concentration that can be used. Here the authors exploit protein induced fluorescent enhancement of DNA sparsely labelled with Cy3 to visualize protein binding and correlate it with changes in DNA conformation.
Collapse
Affiliation(s)
- Dan Song
- Harvard Biophysics Program, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA
| | - Thomas G W Graham
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Seeley G. Mudd Room 204B, Boston, Massachusetts 02115, USA
| |
Collapse
|
12
|
Gambino S, Mousley B, Cathcart L, Winship J, Loparo JJ, Price AC. A single molecule assay for measuring site-specific DNA cleavage. Anal Biochem 2016; 495:3-5. [DOI: 10.1016/j.ab.2015.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/23/2015] [Indexed: 10/22/2022]
|
13
|
Kim H, Loparo JJ. Multistep assembly of DNA condensation clusters by SMC. Nat Commun 2016; 7:10200. [PMID: 26725510 PMCID: PMC4725763 DOI: 10.1038/ncomms10200] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 11/13/2015] [Indexed: 11/09/2022] Open
Abstract
SMC (structural maintenance of chromosomes) family members play essential roles in chromosome condensation, sister chromatid cohesion and DNA repair. It remains unclear how SMCs structure chromosomes and how their mechanochemical cycle regulates their interactions with DNA. Here we used single-molecule fluorescence microscopy to visualize how Bacillus subtilis SMC (BsSMC) interacts with flow-stretched DNAs. We report that BsSMC can slide on DNA, switching between static binding and diffusion. At higher concentrations, BsSMCs form clusters that condense DNA in a weakly ATP-dependent manner. ATP increases the apparent cooperativity of DNA condensation, demonstrating that BsSMC can interact cooperatively through their ATPase head domains. Consistent with these results, ATPase mutants compact DNA more slowly than wild-type BsSMC in the presence of ATP. Our results suggest that transiently static BsSMC molecules can nucleate the formation of clusters that act to locally condense the chromosome while forming long-range DNA bridges. The Structural Maintenance of Chromosomes (SMC) proteins are essential for chromosome condensation, cohesion and DNA repair. Here the authors use single molecule imaging to visualise how Bacillus subtilis SMC interacts with and condenses DNA.
Collapse
Affiliation(s)
- HyeongJun Kim
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|